Personal genomics in 2008: the year in review

In January, an international consortium announced the launch of the 1,000 Genomes Project, which aims to provide a catalogue of human genetic variation. In October, the Personal Genome Project, which hopes to sequence and publish the genomes of as many people as possible, released initial data for ten participants. Meanwhile, as researchers wondered what they could glean from the results coming from personal-genomics companies, the prices of such services dropped. The firm 23andMe, based in Mountain View, California, for instance, now offers personalized genetic information for $399. And finally, two more human genomes — one of an anonymous African, the other an Asian — were decoded, bringing the world’s total of published human genomes to four.

That’s a good start, but these are some additional personal genomics highlights for 2008:

The field became increasingly crowded: 2008 saw the launch of the third major SNP-based personal genomics provider, Navigenics, which brings a touch of old-school medical paternalism to a field that is otherwise commendably libertarian in its approach to giving people access to their own genetic information. This year also saw the emergence of several rather lame attempts to cash in on the personal genomics buzz, including amateurish offerings from SeqWright and the appalling Gene Essence. Finally, we saw competition emerge from an unexpected angle: a free personal genomics service from the Coriell Institute for Medical Research. Unfortunately Coriell shares Navigenics’ regressive attitude towards data release to clients, and requires participants to physically attend an enrollment session in New Jersey – but still, it’s hard to complain about a service that costs nothing.

The costs of large-scale DNA sequencing plummeted: the explosive emergence of so-called “next-generation” DNA sequencing platforms has changed the field of genetics forever. For years researchers have relied on the same basic chemistry to sequence their DNA samples, albeit with successive improvements in sequence quality, speed and price. Now the field has been flooded by technologies based on novel chemistries and offering mind-boggling increases in throughput. This technological change is what made the 1000 Genomes Project feasible, and it is rapidly bringing the costs of large-scale (and even whole-genome) sequencing down towards the point where it can be offered by mainstream personal genomics companies.

Massive genome-wide association studies simultaneously succeeded and failed: dozens of these studies were performed this year on a totally unprecedented scale, requiring large international collaborations and sample sizes in the tens of thousands. They were tremendous successes, in that they yielded hundreds of new genes linked to common diseases, and provided novel insights into the molecular pathways underlying these conditions; but (for various reasons) they simultaneously failed almost entirely to uncover the large-effect risk variants required for personal genomics to provide clinically-relevant predictions.

Open-source personal genomics started to take shape: The SNPedia wiki – a freely accessible repository of information about the most widely-used type of genetic variants, known as SNPs – has been around since 2006, but this is the year that it really came into its own. Firstly, the growing popularity of SNP-based personal genomics meant that suddenly there were lots of people who really wanted to know what all the fuss was about rs4420638; and secondly, the Promethease tool developed by SNPedia co-founder Mike Cariaso made it easy for personal genomics customers to compare their raw data from 23andMe or deCODEme against the entries in the SNPedia database. Promethease lacks the fancy interface and detailed annotation of the personal genomics company databases, but it’s a testament to the bio-hacker spirit – and a sign of things to come.

There were ominous rumblings from regulators: the personal genomics industry has been walking a regulatory tight-rope from the very beginning, wanting to attract customers with the promise of learning information relevant to their health while simultaneously avoiding the regulatory obstacles associated with performing clinical diagnostics. This tension has drawn criticism from a number of angles, most dramatically from regulatory bodies in New York and California: in June, for instance, California’s Department of Public Health sent cease-and-desist letters to 13 direct-to-consumer genetic testing companies insisting on changes to their operating procedures (to variedresponses). Although that little fracas now appears to have simmered down, US federal bodies are also slowly moving into action. The field clearly needs oversight to weed out the bottom-dwellers (see above), but excessively conservative regulation could stifle innovation in the industry, with adverse consequences for the whole field of personalised medicine.

So the end of 2008 sees the field in a state of turmoil, with the industry caught between the excitement of rapidly developing technology on one hand and the deep uncertainty in the regulatory situation on the other. What will 2009 bring? I’ll have some predictions in an upcoming post.
In the meantime, feel free to add your personal highlights in the comments.Subscribe to Genetic Future.alm